BayesPeak: Bayesian Analysis of ChIP-seq Data

This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.

Author
Christiana Spyrou, Jonathan Cairns, Rory Stark, Andy Lynch, Simon Tavar\\'{e},
Date of publication
None
Maintainer
Jonathan Cairns <jonathan.cairns@babraham.ac.uk>
License
GPL (>= 2)
Version
1.26.0

View on Bioconductor

Man pages

bayespeak
BayesPeak - Bayesian analysis of ChIP-seq data
overfitting
Overfitting diagnostic functions
plot.bed
Plot bed file.
plot.job
Plot the called peaks in a job.
plot.PP
Job PP plot.
raw.output
Example raw.output object
raw.output.H3K4me3
Example raw.output object from H3K4me3 data
read.bed
BayesPeak - Bayesian analysis of ChIP-seq data
summarise.peaks
Summarize Peaks

Files in this package

BayesPeak/DESCRIPTION
BayesPeak/NAMESPACE
BayesPeak/R
BayesPeak/R/bayespeak.R
BayesPeak/R/overfitting.R
BayesPeak/R/visuals.R
BayesPeak/build
BayesPeak/build/vignette.rds
BayesPeak/data
BayesPeak/data/datalist
BayesPeak/data/raw.output.H3K4me3.rda
BayesPeak/data/raw.output.rda
BayesPeak/inst
BayesPeak/inst/CITATION
BayesPeak/inst/doc
BayesPeak/inst/doc/BayesPeak.R
BayesPeak/inst/doc/BayesPeak.Rnw
BayesPeak/inst/doc/BayesPeak.pdf
BayesPeak/inst/extdata
BayesPeak/inst/extdata/H3K4me3reduced.bed
BayesPeak/inst/extdata/Inputreduced.bed
BayesPeak/man
BayesPeak/man/bayespeak.Rd
BayesPeak/man/overfitting.Rd
BayesPeak/man/plot.PP.Rd
BayesPeak/man/plot.bed.Rd
BayesPeak/man/plot.job.Rd
BayesPeak/man/raw.output.H3K4me3.Rd
BayesPeak/man/raw.output.Rd
BayesPeak/man/read.bed.Rd
BayesPeak/man/summarise.peaks.Rd
BayesPeak/src
BayesPeak/src/bayespeak.c
BayesPeak/src/bayespeak_gsl.h
BayesPeak/vignettes
BayesPeak/vignettes/BayesPeak.Rnw
BayesPeak/vignettes/BayesPeak.bib
BayesPeak/vignettes/OF.png
BayesPeak/vignettes/changelog.txt
BayesPeak/vignettes/regionOFdiag.pdf